# Stk11 KO Experiments

Mouse BLA was injected bilaterally with AAV5-CamKIIa-Cre-GFP (Cre Group) or AAV5-CamKIIa-GFP (GFP Group/ Control). 

## File info

1. *animal_info.csv* : Information about the group identity of each animal as well as their saccharin consumption (relative to nightly water consumption) and whether or not they learned the CTA.
2. *Stk11_Project_project.p* : blechpy.Project object that houses the project information and is used for analysis.
3. *hmm_overview.csv* : table of HMM metadata for models stored in *All_spike_and_HMM_data.hdf5*.
4. *All_spike_and_HMM_data.hdf5* : Contains all spike arrays and fitted HMM model parameters used in the analysis in the manuscript.
5. *data_process.py* : example script for intial data extraction and processing with blechpy package
6. *Manuscript Source Data* : tables of extracted data metrics used for creating the figures presented in the manuscript
7. *Stk11_Project_analysis* : All analysis results and data files needed for replication
8. **Animal Folders** : (RN5, RN10, etc). raw and spike sorted data for each recording for each animal. Also contains blechpy data objects *_experiment.p* and *_dataset.p* files. Also separate animal *_metadata.p* files for surgery and consumption.
9. *_experiment.p* : blechpy.Experiment object file. These files order recordings and provide filepaths to analysis software.
10. *_dataset.p* : blechpy.Dataset object files. These files facilitate processing of individual recordings, and contain most recording relevant metadata including electrode locations and trial info.

## Analysis Code

Analysis was done using the `blechpy` python package available on PyPi and [github](https://github.com/nubs01/blechpy).
Additional -- project/manuscript specific -- analysis code is also available on GitHub in the [cta_analysis](https://github.com/nubs01/cta_analysis) repository.

## Recording Info

Recordings were done using the Intan RHD2000 evaluation system. 16 electrode
bundles were implanted bilaterally into GC and tastes were delivered directly
onto the toungue via intraoral canulae (IOC). Trial times mark stimulus offset.


All animals underwent 4 recording sessions over 3 days:

1. 4taste_preCTA: *Day 1*: animal is presented with 60 trials in which 4 taste solutions are given: NaCl, Citric Acid, Quinine and Water (15 trials each)
2. ctaTrain: *Day 2*: animal is presented with 60 presentations of Saccharin solution (followed by LiCl injection)
3. ctaTest/SaccTest: *Day 3*: animal is presented with 15 deliveries of Saccharin solution (to observe post-CTA response)
4. 4taste_postCTA: *Day 3*: same as recording session 1, but after CTA training 
